Visualise genotype data for a subset of accessions around specific genomic regions¶

Note

This use case assumes that a genomic region of interest has already been identified. This can be done from either of the following use cases:

This specific example continues on from Visualise the location of a subset of markers or a region

Click back onto the Explore tab and search for a genotype dataset and add it to the view then in the view, click on the axis title. This dataset can be found on agg.plantinformatics.io

Hordeum vulgare - MorexV3 - Genotypes - AGG Filled Release 1

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Within the window that pops up, click the far right hand button up the top to open the axis

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Close the axis title menu by clicking the "X" button in the top right corner

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Click and drag over the area of interest along the axis to select a region on the chromosome and click the zoom button below the axis

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If needed, reselect a given area to zoom in further to select only the required features

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Click the Genotype tab in the right hand panel to switch to Genotype view then press the button highlighted by the red arrow in the screenshot

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In the resulting box that pops up, click desired samples (ctrl click to select multiple samples), the click "VCF lookup" button at the bottom of the pop up window. The selected samples will display in the bottom text box

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Genotypes for the selected samples in the selected genomic region are displayed in the right hand panel

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